HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) All Versions of this Article: 10/3/169    most recent 00120.2001v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (31) Citing Articles via Google Scholar Google Scholar Articles by Manduchi, E. Articles by Stoeckert, C. J. Search for Related Content PubMed PubMed Citation Articles by Manduchi, E. Articles by Stoeckert, C. J., JR.

Comparison of different labeling methods for two-channel high-density microarray experiments

¹ Center for Bioinformatics, Philadelphia, Pennsylvania 19104
² Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104

In this report we evaluate three methods for labeling nucleic acids to be hybridized to a cDNA microarray: direct labeling, indirect amino-allyl labeling, and the dendrimer labeling method (Genisphere). The dendrimer method requires the smallest quantity of sample, 2.5 µg of total RNA compared with 20 µg with the direct or indirect methods. Therefore, we wanted to know whether the performance of the dendrimer method is comparable to the other methods, or whether significant information is lost. Performance can be considered in terms of sensitivity, dynamic range, and reproducibility of the quantitative signals for gene intensity. We compared the three labeling methods by generating three sets of eight self-to-self hybridizations using the same total RNA sample in all cases ("replicate study"). In our analysis, we controlled for the effects of print-tip and background subtraction biases. We also performed a smaller study, namely, a dilution series study with five dilution points per labeling method, to evaluate one aspect of predictive ability. From the replicate study, the dendrimer method appeared to perform as well, and often better, with respect to reproducibility and ability to detect expression. However, in the dilution series study, this method was outperformed by the other two in terms of predictive ability and did not perform very well. These findings are helping to guide our decisions on what labeling method to use for subsequent studies, based on the purpose of a specific study and its limitations in terms of available material.

evaluation of labeling protocols; direct labeling; indirect amino-allyl labeling; dendrimer labeling

This article has been cited by other articles:

				K. K. Dobbin, E. S. Kawasaki, D. W. Petersen, and R. M. Simon Characterizing dye bias in microarray experiments Bioinformatics, May 15, 2005; 21(10): 2430 - 2437. [Abstract] [Full Text] [PDF]

				M. Ohsugi, C. Cras-Meneur, Y. Zhou, E. Bernal-Mizrachi, J. D. Johnson, D. S. Luciani, K. S. Polonsky, and M. A. Permutt Reduced Expression of the Insulin Receptor in Mouse Insulinoma (MIN6) Cells Reveals Multiple Roles of Insulin Signaling in Gene Expression, Proliferation, Insulin Content, and Secretion J. Biol. Chem., February 11, 2005; 280(6): 4992 - 5003. [Abstract] [Full Text] [PDF]

				M. Ohsugi, C. Cras-Meneur, Y. Zhou, W. Warren, E. Bernal-Mizrachi, and M. A. Permutt Glucose and Insulin Treatment of Insulinoma Cells Results in Transcriptional Regulation of a Common Set of Genes Diabetes, June 1, 2004; 53(6): 1496 - 1508. [Abstract] [Full Text] [PDF]

				T. Xu, C.-T. Shu, E. Purdom, D. Dang, D. Ilsley, Y. Guo, J. Weber, S. P. Holmes, and P. P. Lee Microarray Analysis Reveals Differences in Gene Expression of Circulating CD8+ T Cells in Melanoma Patients and Healthy Donors Cancer Res., May 15, 2004; 64(10): 3661 - 3667. [Abstract] [Full Text] [PDF]

				F. Yadetie, A. Laegreid, I. Bakke, W. Kusnierczyk, J. Komorowski, H. L. Waldum, and A. K. Sandvik Liver gene expression in rats in response to the peroxisome proliferator-activated receptor-{alpha} agonist ciprofibrate Physiol Genomics, September 29, 2003; 15(1): 9 - 19. [Abstract] [Full Text] [PDF]

				K. Dobbin, J. H. Shih, and R. Simon Questions and Answers on Design of Dual-Label Microarrays for Identifying Differentially Expressed Genes J Natl Cancer Inst, September 17, 2003; 95(18): 1362 - 1369. [Full Text] [PDF]

				K. H. Kaestner, C. S. Lee, L. M. Scearce, J. E. Brestelli, A. Arsenlis, P. P. Le, K. A. Lantz, J. Crabtree, A. Pizarro, J. Mazzarelli, et al. Transcriptional Program of the Endocrine Pancreas in Mice and Humans Diabetes, July 1, 2003; 52(7): 1604 - 1610. [Abstract] [Full Text] [PDF]

				L. Smith, P. Underhill, C. Pritchard, Z. Tymowska-Lalanne, S. Abdul-Hussein, H. Hilton, L. Winchester, D. Williams, T. Freeman, S. Webb, et al. Single primer amplification (SPA) of cDNA for microarray expression analysis Nucleic Acids Res., February 1, 2003; 31(3): e9 - e9. [Abstract] [Full Text] [PDF]